Starting phenix.real_space_refine on Fri May 9 22:38:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ya3_39090/05_2025/8ya3_39090.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ya3_39090/05_2025/8ya3_39090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ya3_39090/05_2025/8ya3_39090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ya3_39090/05_2025/8ya3_39090.map" model { file = "/net/cci-nas-00/data/ceres_data/8ya3_39090/05_2025/8ya3_39090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ya3_39090/05_2025/8ya3_39090.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2700 2.51 5 N 668 2.21 5 O 677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4060 Number of models: 1 Model: "" Number of chains: 3 Chain: "Y" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3165 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 20, 'TRANS': 385} Chain breaks: 2 Chain: "E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 480 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "B" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 415 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain breaks: 2 Time building chain proxies: 3.00, per 1000 atoms: 0.74 Number of scatterers: 4060 At special positions: 0 Unit cell: (91.524, 69.432, 88.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 677 8.00 N 668 7.00 C 2700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 466.2 milliseconds 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 954 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 1 sheets defined 71.9% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'Y' and resid 2 through 11 Processing helix chain 'Y' and resid 11 through 33 Processing helix chain 'Y' and resid 74 through 88 removed outlier: 3.568A pdb=" N GLN Y 88 " --> pdb=" O VAL Y 84 " (cutoff:3.500A) Processing helix chain 'Y' and resid 92 through 100 Processing helix chain 'Y' and resid 102 through 134 Processing helix chain 'Y' and resid 145 through 173 Processing helix chain 'Y' and resid 177 through 202 removed outlier: 3.647A pdb=" N ILE Y 181 " --> pdb=" O ASN Y 177 " (cutoff:3.500A) Proline residue: Y 192 - end of helix Processing helix chain 'Y' and resid 213 through 236 Processing helix chain 'Y' and resid 271 through 292 Proline residue: Y 284 - end of helix removed outlier: 3.519A pdb=" N GLY Y 292 " --> pdb=" O ALA Y 288 " (cutoff:3.500A) Processing helix chain 'Y' and resid 294 through 304 removed outlier: 3.579A pdb=" N LEU Y 298 " --> pdb=" O ASN Y 294 " (cutoff:3.500A) Processing helix chain 'Y' and resid 310 through 331 removed outlier: 3.651A pdb=" N ILE Y 314 " --> pdb=" O VAL Y 310 " (cutoff:3.500A) Processing helix chain 'Y' and resid 332 through 343 removed outlier: 3.553A pdb=" N GLN Y 343 " --> pdb=" O ASN Y 339 " (cutoff:3.500A) Processing helix chain 'Y' and resid 353 through 390 removed outlier: 4.028A pdb=" N GLN Y 357 " --> pdb=" O GLY Y 353 " (cutoff:3.500A) Proline residue: Y 382 - end of helix removed outlier: 3.883A pdb=" N PHE Y 388 " --> pdb=" O PHE Y 384 " (cutoff:3.500A) Processing helix chain 'Y' and resid 399 through 422 removed outlier: 3.907A pdb=" N LEU Y 403 " --> pdb=" O GLY Y 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 16 removed outlier: 3.562A pdb=" N LYS E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 59 Processing helix chain 'B' and resid 3 through 19 Processing helix chain 'B' and resid 36 through 41 Processing sheet with id=AA1, first strand: chain 'Y' and resid 261 through 265 removed outlier: 3.634A pdb=" N PHE Y 238 " --> pdb=" O SER E 19 " (cutoff:3.500A) 287 hydrogen bonds defined for protein. 861 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1227 1.34 - 1.46: 811 1.46 - 1.57: 2084 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 4150 Sorted by residual: bond pdb=" CB THR Y 323 " pdb=" CG2 THR Y 323 " ideal model delta sigma weight residual 1.521 1.433 0.088 3.30e-02 9.18e+02 7.04e+00 bond pdb=" CG PRO Y 273 " pdb=" CD PRO Y 273 " ideal model delta sigma weight residual 1.503 1.431 0.072 3.40e-02 8.65e+02 4.43e+00 bond pdb=" CB PRO Y 76 " pdb=" CG PRO Y 76 " ideal model delta sigma weight residual 1.492 1.405 0.087 5.00e-02 4.00e+02 3.05e+00 bond pdb=" CA HIS Y 424 " pdb=" C HIS Y 424 " ideal model delta sigma weight residual 1.531 1.514 0.017 1.12e-02 7.97e+03 2.32e+00 bond pdb=" CB GLN Y 235 " pdb=" CG GLN Y 235 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.28e+00 ... (remaining 4145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 5299 1.74 - 3.47: 272 3.47 - 5.21: 52 5.21 - 6.95: 10 6.95 - 8.69: 5 Bond angle restraints: 5638 Sorted by residual: angle pdb=" N VAL Y 421 " pdb=" CA VAL Y 421 " pdb=" C VAL Y 421 " ideal model delta sigma weight residual 111.05 118.75 -7.70 1.25e+00 6.40e-01 3.79e+01 angle pdb=" C LEU Y 420 " pdb=" N VAL Y 421 " pdb=" CA VAL Y 421 " ideal model delta sigma weight residual 120.47 125.81 -5.34 1.58e+00 4.01e-01 1.14e+01 angle pdb=" CA PRO Y 284 " pdb=" C PRO Y 284 " pdb=" N PRO Y 285 " ideal model delta sigma weight residual 117.93 121.97 -4.04 1.20e+00 6.94e-01 1.13e+01 angle pdb=" C GLN Y 142 " pdb=" N ASN Y 143 " pdb=" CA ASN Y 143 " ideal model delta sigma weight residual 121.80 129.95 -8.15 2.44e+00 1.68e-01 1.12e+01 angle pdb=" C LYS Y 422 " pdb=" N ARG Y 423 " pdb=" CA ARG Y 423 " ideal model delta sigma weight residual 120.28 125.00 -4.72 1.44e+00 4.82e-01 1.07e+01 ... (remaining 5633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 2087 17.00 - 34.00: 257 34.00 - 51.00: 69 51.00 - 68.00: 6 68.00 - 84.99: 3 Dihedral angle restraints: 2422 sinusoidal: 939 harmonic: 1483 Sorted by residual: dihedral pdb=" CA GLY Y 344 " pdb=" C GLY Y 344 " pdb=" N GLY Y 345 " pdb=" CA GLY Y 345 " ideal model delta harmonic sigma weight residual -180.00 -154.57 -25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA PHE B 44 " pdb=" C PHE B 44 " pdb=" N GLU B 45 " pdb=" CA GLU B 45 " ideal model delta harmonic sigma weight residual 180.00 161.80 18.20 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA GLN Y 65 " pdb=" C GLN Y 65 " pdb=" N ASN Y 66 " pdb=" CA ASN Y 66 " ideal model delta harmonic sigma weight residual 180.00 162.77 17.23 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 2419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 386 0.039 - 0.079: 197 0.079 - 0.118: 64 0.118 - 0.157: 27 0.157 - 0.196: 8 Chirality restraints: 682 Sorted by residual: chirality pdb=" CB ILE Y 397 " pdb=" CA ILE Y 397 " pdb=" CG1 ILE Y 397 " pdb=" CG2 ILE Y 397 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" CA VAL Y 36 " pdb=" N VAL Y 36 " pdb=" C VAL Y 36 " pdb=" CB VAL Y 36 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CA THR Y 323 " pdb=" N THR Y 323 " pdb=" C THR Y 323 " pdb=" CB THR Y 323 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 8.06e-01 ... (remaining 679 not shown) Planarity restraints: 689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO Y 284 " 0.049 5.00e-02 4.00e+02 7.22e-02 8.34e+00 pdb=" N PRO Y 285 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO Y 285 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO Y 285 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL Y 36 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO Y 37 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO Y 37 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO Y 37 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU Y 391 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO Y 392 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO Y 392 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO Y 392 " -0.028 5.00e-02 4.00e+02 ... (remaining 686 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1102 2.79 - 3.32: 3770 3.32 - 3.85: 6689 3.85 - 4.37: 7019 4.37 - 4.90: 12452 Nonbonded interactions: 31032 Sorted by model distance: nonbonded pdb=" O LEU Y 364 " pdb=" OG1 THR Y 368 " model vdw 2.266 3.040 nonbonded pdb=" O TRP Y 299 " pdb=" OG1 THR Y 303 " model vdw 2.288 3.040 nonbonded pdb=" CZ PHE Y 280 " pdb=" CD1 LEU B 13 " model vdw 2.336 3.760 nonbonded pdb=" NE2 GLN Y 85 " pdb=" OH TYR Y 326 " model vdw 2.360 3.120 nonbonded pdb=" CE1 PHE Y 280 " pdb=" CD1 LEU B 13 " model vdw 2.385 3.760 ... (remaining 31027 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.220 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.088 4150 Z= 0.370 Angle : 0.933 8.687 5638 Z= 0.520 Chirality : 0.057 0.196 682 Planarity : 0.008 0.072 689 Dihedral : 15.754 84.995 1468 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.23 % Allowed : 21.77 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.31), residues: 505 helix: -1.30 (0.21), residues: 358 sheet: -0.13 (1.71), residues: 10 loop : -2.83 (0.50), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP Y 98 HIS 0.004 0.001 HIS B 67 PHE 0.019 0.002 PHE Y 328 TYR 0.013 0.002 TYR Y 326 ARG 0.002 0.000 ARG Y 366 Details of bonding type rmsd hydrogen bonds : bond 0.11954 ( 287) hydrogen bonds : angle 5.69910 ( 861) covalent geometry : bond 0.00898 ( 4150) covalent geometry : angle 0.93317 ( 5638) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 411 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7389 (tm-30) REVERT: E 54 LEU cc_start: 0.9074 (tp) cc_final: 0.8780 (tt) REVERT: B 49 LEU cc_start: 0.9302 (mt) cc_final: 0.8703 (mm) outliers start: 1 outliers final: 1 residues processed: 59 average time/residue: 0.2452 time to fit residues: 17.2753 Evaluate side-chains 45 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 385 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 66 ASN Y 85 GLN Y 235 GLN Y 267 ASN Y 387 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.081778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.063609 restraints weight = 12013.754| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.73 r_work: 0.2992 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4150 Z= 0.135 Angle : 0.561 5.395 5638 Z= 0.301 Chirality : 0.041 0.151 682 Planarity : 0.005 0.048 689 Dihedral : 5.042 39.522 553 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.27 % Allowed : 22.22 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.36), residues: 505 helix: 0.99 (0.25), residues: 365 sheet: 0.32 (1.79), residues: 10 loop : -2.43 (0.52), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 98 HIS 0.002 0.000 HIS Y 424 PHE 0.017 0.001 PHE Y 291 TYR 0.009 0.001 TYR Y 359 ARG 0.003 0.000 ARG Y 423 Details of bonding type rmsd hydrogen bonds : bond 0.04830 ( 287) hydrogen bonds : angle 4.07953 ( 861) covalent geometry : bond 0.00287 ( 4150) covalent geometry : angle 0.56117 ( 5638) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: Y 250 GLU cc_start: 0.8043 (tt0) cc_final: 0.7770 (tm-30) REVERT: Y 326 TYR cc_start: 0.9078 (t80) cc_final: 0.8872 (t80) REVERT: E 54 LEU cc_start: 0.9025 (tp) cc_final: 0.8796 (tt) REVERT: B 43 MET cc_start: 0.7666 (ptp) cc_final: 0.7360 (ptp) outliers start: 10 outliers final: 6 residues processed: 63 average time/residue: 0.1706 time to fit residues: 13.5555 Evaluate side-chains 53 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 312 MET Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 46 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.082073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.064062 restraints weight = 12018.131| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.67 r_work: 0.3001 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4150 Z= 0.136 Angle : 0.525 5.452 5638 Z= 0.279 Chirality : 0.041 0.146 682 Planarity : 0.004 0.044 689 Dihedral : 4.642 38.726 553 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.72 % Allowed : 22.68 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.38), residues: 505 helix: 1.88 (0.26), residues: 365 sheet: 0.57 (1.89), residues: 10 loop : -2.05 (0.53), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 98 HIS 0.001 0.000 HIS Y 424 PHE 0.011 0.001 PHE Y 112 TYR 0.009 0.001 TYR Y 326 ARG 0.002 0.000 ARG Y 423 Details of bonding type rmsd hydrogen bonds : bond 0.04529 ( 287) hydrogen bonds : angle 3.82140 ( 861) covalent geometry : bond 0.00302 ( 4150) covalent geometry : angle 0.52519 ( 5638) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.483 Fit side-chains REVERT: Y 90 ASP cc_start: 0.8211 (m-30) cc_final: 0.7848 (t0) REVERT: Y 130 TYR cc_start: 0.8301 (t80) cc_final: 0.8062 (t80) REVERT: E 10 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8734 (mm-30) REVERT: E 54 LEU cc_start: 0.9097 (tp) cc_final: 0.8856 (tt) REVERT: B 43 MET cc_start: 0.7689 (ptp) cc_final: 0.7474 (ptp) outliers start: 12 outliers final: 7 residues processed: 62 average time/residue: 0.1543 time to fit residues: 12.3148 Evaluate side-chains 54 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 418 SER Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 46 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.0370 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.083083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.064905 restraints weight = 11988.066| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.72 r_work: 0.3006 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4150 Z= 0.126 Angle : 0.527 5.463 5638 Z= 0.277 Chirality : 0.040 0.139 682 Planarity : 0.004 0.042 689 Dihedral : 4.181 20.712 551 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.40 % Allowed : 22.68 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.38), residues: 505 helix: 2.25 (0.27), residues: 363 sheet: 0.69 (1.86), residues: 10 loop : -1.92 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 98 HIS 0.001 0.000 HIS Y 424 PHE 0.010 0.001 PHE E 43 TYR 0.008 0.001 TYR Y 77 ARG 0.002 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.04352 ( 287) hydrogen bonds : angle 3.72682 ( 861) covalent geometry : bond 0.00277 ( 4150) covalent geometry : angle 0.52735 ( 5638) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.421 Fit side-chains REVERT: Y 90 ASP cc_start: 0.8220 (m-30) cc_final: 0.7827 (t0) REVERT: Y 130 TYR cc_start: 0.8303 (t80) cc_final: 0.8032 (t80) REVERT: E 54 LEU cc_start: 0.9076 (tp) cc_final: 0.8851 (tt) outliers start: 15 outliers final: 9 residues processed: 62 average time/residue: 0.1328 time to fit residues: 10.9381 Evaluate side-chains 55 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 418 SER Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.0770 chunk 30 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 0.0870 chunk 4 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.083602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.065578 restraints weight = 12115.950| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.71 r_work: 0.3028 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4150 Z= 0.118 Angle : 0.521 5.745 5638 Z= 0.274 Chirality : 0.040 0.139 682 Planarity : 0.004 0.042 689 Dihedral : 4.136 20.284 551 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.40 % Allowed : 21.54 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.38), residues: 505 helix: 2.55 (0.26), residues: 359 sheet: 0.24 (1.54), residues: 14 loop : -1.74 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 98 HIS 0.001 0.000 HIS Y 424 PHE 0.009 0.001 PHE Y 112 TYR 0.007 0.001 TYR Y 77 ARG 0.002 0.000 ARG Y 423 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 287) hydrogen bonds : angle 3.65773 ( 861) covalent geometry : bond 0.00255 ( 4150) covalent geometry : angle 0.52094 ( 5638) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.479 Fit side-chains REVERT: Y 72 MET cc_start: 0.9233 (tpt) cc_final: 0.9029 (tpt) REVERT: Y 90 ASP cc_start: 0.8127 (m-30) cc_final: 0.7779 (t0) REVERT: Y 130 TYR cc_start: 0.8302 (t80) cc_final: 0.8010 (t80) REVERT: Y 173 LYS cc_start: 0.8673 (mtmt) cc_final: 0.8411 (mttp) REVERT: Y 336 MET cc_start: 0.8448 (ttm) cc_final: 0.8035 (tpt) REVERT: E 14 GLU cc_start: 0.8388 (tp30) cc_final: 0.8050 (tm-30) outliers start: 15 outliers final: 14 residues processed: 56 average time/residue: 0.1296 time to fit residues: 9.5891 Evaluate side-chains 59 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 403 LEU Chi-restraints excluded: chain Y residue 418 SER Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 46 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 0.0370 chunk 4 optimal weight: 0.0270 chunk 41 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.084531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.066878 restraints weight = 11925.499| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.67 r_work: 0.3061 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 4150 Z= 0.114 Angle : 0.528 7.827 5638 Z= 0.272 Chirality : 0.039 0.137 682 Planarity : 0.004 0.042 689 Dihedral : 4.047 21.415 551 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.72 % Allowed : 21.77 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.38), residues: 505 helix: 2.70 (0.26), residues: 359 sheet: 0.43 (1.52), residues: 14 loop : -1.57 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 98 HIS 0.001 0.000 HIS B 42 PHE 0.008 0.001 PHE E 43 TYR 0.007 0.001 TYR Y 233 ARG 0.003 0.000 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 287) hydrogen bonds : angle 3.58145 ( 861) covalent geometry : bond 0.00241 ( 4150) covalent geometry : angle 0.52768 ( 5638) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.436 Fit side-chains REVERT: Y 90 ASP cc_start: 0.8042 (m-30) cc_final: 0.7755 (t0) REVERT: Y 130 TYR cc_start: 0.8280 (t80) cc_final: 0.7947 (t80) REVERT: Y 173 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8426 (mttp) REVERT: Y 336 MET cc_start: 0.8589 (ttm) cc_final: 0.8151 (tpt) REVERT: E 14 GLU cc_start: 0.8386 (tp30) cc_final: 0.8091 (tm-30) outliers start: 12 outliers final: 10 residues processed: 58 average time/residue: 0.1385 time to fit residues: 10.6301 Evaluate side-chains 56 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 418 SER Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 46 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.0770 chunk 47 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.083743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.065757 restraints weight = 12051.975| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.71 r_work: 0.3038 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4150 Z= 0.121 Angle : 0.524 7.469 5638 Z= 0.271 Chirality : 0.040 0.130 682 Planarity : 0.004 0.042 689 Dihedral : 3.978 20.037 551 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.40 % Allowed : 21.09 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.38), residues: 505 helix: 2.66 (0.26), residues: 365 sheet: 0.51 (1.49), residues: 14 loop : -1.47 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 98 HIS 0.001 0.000 HIS Y 424 PHE 0.028 0.001 PHE E 43 TYR 0.007 0.001 TYR Y 77 ARG 0.002 0.000 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 287) hydrogen bonds : angle 3.60142 ( 861) covalent geometry : bond 0.00266 ( 4150) covalent geometry : angle 0.52358 ( 5638) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.429 Fit side-chains REVERT: Y 90 ASP cc_start: 0.8034 (m-30) cc_final: 0.7754 (t0) REVERT: Y 130 TYR cc_start: 0.8295 (t80) cc_final: 0.7975 (t80) REVERT: Y 173 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8427 (mttp) REVERT: Y 336 MET cc_start: 0.8583 (ttm) cc_final: 0.8120 (tpt) REVERT: E 14 GLU cc_start: 0.8401 (tp30) cc_final: 0.8134 (tm-30) REVERT: E 51 ILE cc_start: 0.9175 (mm) cc_final: 0.8953 (tt) outliers start: 15 outliers final: 13 residues processed: 58 average time/residue: 0.1269 time to fit residues: 10.1146 Evaluate side-chains 59 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 403 LEU Chi-restraints excluded: chain Y residue 418 SER Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 46 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.0870 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.083617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.065276 restraints weight = 11885.127| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.73 r_work: 0.3023 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4150 Z= 0.132 Angle : 0.534 7.467 5638 Z= 0.276 Chirality : 0.040 0.131 682 Planarity : 0.004 0.042 689 Dihedral : 3.971 20.285 551 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.40 % Allowed : 21.77 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.38), residues: 505 helix: 2.72 (0.26), residues: 365 sheet: 0.90 (1.45), residues: 14 loop : -1.41 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 98 HIS 0.001 0.000 HIS Y 424 PHE 0.024 0.001 PHE E 43 TYR 0.007 0.001 TYR Y 77 ARG 0.001 0.000 ARG Y 423 Details of bonding type rmsd hydrogen bonds : bond 0.04204 ( 287) hydrogen bonds : angle 3.62452 ( 861) covalent geometry : bond 0.00299 ( 4150) covalent geometry : angle 0.53353 ( 5638) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.406 Fit side-chains REVERT: Y 72 MET cc_start: 0.9278 (tpt) cc_final: 0.9045 (tpt) REVERT: Y 90 ASP cc_start: 0.7998 (m-30) cc_final: 0.7739 (t0) REVERT: Y 130 TYR cc_start: 0.8314 (t80) cc_final: 0.8011 (t80) REVERT: Y 173 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8417 (mttp) REVERT: Y 336 MET cc_start: 0.8595 (ttm) cc_final: 0.8099 (tpt) REVERT: E 14 GLU cc_start: 0.8419 (tp30) cc_final: 0.8155 (tm-30) REVERT: E 51 ILE cc_start: 0.9152 (mm) cc_final: 0.8921 (tt) outliers start: 15 outliers final: 15 residues processed: 58 average time/residue: 0.1116 time to fit residues: 8.8464 Evaluate side-chains 62 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 139 MET Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 403 LEU Chi-restraints excluded: chain Y residue 418 SER Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 51 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.082412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.064182 restraints weight = 12058.440| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.69 r_work: 0.2999 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4150 Z= 0.157 Angle : 0.576 10.330 5638 Z= 0.297 Chirality : 0.041 0.132 682 Planarity : 0.004 0.042 689 Dihedral : 3.984 21.168 551 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.63 % Allowed : 22.22 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.38), residues: 505 helix: 2.66 (0.26), residues: 365 sheet: 1.01 (1.49), residues: 14 loop : -1.41 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 98 HIS 0.003 0.001 HIS B 42 PHE 0.025 0.001 PHE E 43 TYR 0.007 0.001 TYR Y 77 ARG 0.001 0.000 ARG Y 423 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 287) hydrogen bonds : angle 3.70858 ( 861) covalent geometry : bond 0.00363 ( 4150) covalent geometry : angle 0.57630 ( 5638) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.486 Fit side-chains REVERT: Y 72 MET cc_start: 0.9213 (tpt) cc_final: 0.8994 (tpt) REVERT: Y 90 ASP cc_start: 0.7995 (m-30) cc_final: 0.7728 (t0) REVERT: Y 130 TYR cc_start: 0.8334 (t80) cc_final: 0.8048 (t80) REVERT: Y 173 LYS cc_start: 0.8660 (mtmt) cc_final: 0.8404 (mttp) REVERT: Y 336 MET cc_start: 0.8570 (ttm) cc_final: 0.8065 (tpt) REVERT: E 14 GLU cc_start: 0.8397 (tp30) cc_final: 0.8141 (tm-30) REVERT: E 51 ILE cc_start: 0.9178 (mm) cc_final: 0.8938 (tt) outliers start: 16 outliers final: 13 residues processed: 56 average time/residue: 0.1211 time to fit residues: 9.3239 Evaluate side-chains 57 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 139 MET Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 418 SER Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 19 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.0370 chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.084127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.066133 restraints weight = 11913.160| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.69 r_work: 0.3045 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4150 Z= 0.117 Angle : 0.573 13.858 5638 Z= 0.288 Chirality : 0.039 0.132 682 Planarity : 0.004 0.042 689 Dihedral : 3.865 18.309 551 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.27 % Allowed : 23.81 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.38), residues: 505 helix: 2.75 (0.26), residues: 364 sheet: 1.14 (1.48), residues: 14 loop : -1.23 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Y 98 HIS 0.001 0.000 HIS B 42 PHE 0.024 0.001 PHE E 43 TYR 0.008 0.001 TYR Y 77 ARG 0.001 0.000 ARG Y 423 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 287) hydrogen bonds : angle 3.55548 ( 861) covalent geometry : bond 0.00256 ( 4150) covalent geometry : angle 0.57305 ( 5638) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.472 Fit side-chains REVERT: Y 72 MET cc_start: 0.9253 (tpt) cc_final: 0.9046 (tpt) REVERT: Y 90 ASP cc_start: 0.7897 (m-30) cc_final: 0.7694 (t0) REVERT: Y 130 TYR cc_start: 0.8316 (t80) cc_final: 0.8058 (t80) REVERT: Y 173 LYS cc_start: 0.8658 (mtmt) cc_final: 0.8412 (mttp) REVERT: Y 336 MET cc_start: 0.8575 (ttm) cc_final: 0.8158 (tpt) REVERT: E 14 GLU cc_start: 0.8335 (tp30) cc_final: 0.8110 (tm-30) REVERT: B 48 PHE cc_start: 0.7560 (t80) cc_final: 0.6943 (t80) outliers start: 10 outliers final: 10 residues processed: 55 average time/residue: 0.1214 time to fit residues: 9.1354 Evaluate side-chains 56 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 418 SER Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.083357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.065012 restraints weight = 12045.512| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.75 r_work: 0.3014 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4150 Z= 0.136 Angle : 0.578 13.289 5638 Z= 0.292 Chirality : 0.040 0.131 682 Planarity : 0.004 0.042 689 Dihedral : 3.851 20.035 551 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.72 % Allowed : 23.13 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.38), residues: 505 helix: 2.77 (0.26), residues: 365 sheet: 1.11 (1.50), residues: 14 loop : -1.18 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 98 HIS 0.001 0.000 HIS Y 424 PHE 0.023 0.001 PHE E 43 TYR 0.007 0.001 TYR Y 77 ARG 0.001 0.000 ARG Y 423 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 287) hydrogen bonds : angle 3.60897 ( 861) covalent geometry : bond 0.00311 ( 4150) covalent geometry : angle 0.57768 ( 5638) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2146.62 seconds wall clock time: 37 minutes 58.06 seconds (2278.06 seconds total)